PDBsum entry 2gjd

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protein Protein-protein interface(s) links
Ligase PDB id
Protein chains
155 a.a. *
Waters ×473
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Distinct functional domains of ubc9 dictate cell survival and resistance to genotoxic stress
Structure: Ubiquitin-conjugating enzyme e2-18 kda. Chain: a, b, c, d. Synonym: ubiquitin- protein ligase, ubiquitin carrier protein. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ubc9. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
1.75Å     R-factor:   0.210     R-free:   0.230
Authors: R.C.Van Waardenburg,D.M.Duda,C.S.Lancaster,B.A.Schulman, M.A.Bjornsti
Key ref: R.C.van Waardenburg et al. (2006). Distinct functional domains of Ubc9 dictate cell survival and resistance to genotoxic stress. Mol Cell Biol, 26, 4958-4969. PubMed id: 16782883
30-Mar-06     Release date:   04-Jul-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P50623  (UBC9_YEAST) -  SUMO-conjugating enzyme UBC9
157 a.a.
155 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   2 terms 
  Biological process     cell cycle   5 terms 
  Biochemical function     nucleotide binding     5 terms  


Mol Cell Biol 26:4958-4969 (2006)
PubMed id: 16782883  
Distinct functional domains of Ubc9 dictate cell survival and resistance to genotoxic stress.
R.C.van Waardenburg, D.M.Duda, C.S.Lancaster, B.A.Schulman, M.A.Bjornsti.
Covalent modification with SUMO alters protein function, intracellular localization, or protein-protein interactions. Target recognition is determined, in part, by the SUMO E2 enzyme, Ubc9, while Siz/Pias E3 ligases may facilitate select interactions by acting as substrate adaptors. A yeast conditional Ubc9P(123)L mutant was viable at 36 degrees C yet exhibited enhanced sensitivity to DNA damage. To define functional domains in Ubc9 that dictate cellular responses to genotoxic stress versus those necessary for cell viability, a 1.75-A structure of yeast Ubc9 that demonstrated considerable conservation of backbone architecture with human Ubc9 was solved. Nevertheless, differences in side chain geometry/charge guided the design of human/yeast chimeras, where swapping domains implicated in (i) binding residues within substrates that flank canonical SUMOylation sites, (ii) interactions with the RanBP2 E3 ligase, and (iii) binding of the heterodimeric E1 and SUMO had distinct effects on cell growth and resistance to DNA-damaging agents. Our findings establish a functional interaction between N-terminal and substrate-binding domains of Ubc9 and distinguish the activities of E3 ligases Siz1 and Siz2 in regulating cellular responses to genotoxic stress.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21483811 M.T.Lee, A.A.Bakir, K.N.Nguyen, and J.Bachant (2011).
The SUMO isopeptidase Ulp2p is required to prevent recombination-induced chromosome segregation lethality following DNA replication stress.
  PLoS Genet, 7, e1001355.  
21209884 J.Wang, A.M.Taherbhoy, H.W.Hunt, S.N.Seyedin, D.W.Miller, D.J.Miller, D.T.Huang, and B.A.Schulman (2010).
Crystal structure of UBA2(ufd)-Ubc9: insights into E1-E2 interactions in Sumo pathways.
  PLoS One, 5, e15805.  
  20865051 M.Tozluo─člu, E.Karaca, R.Nussinov, and T.Halilo─člu (2010).
A mechanistic view of the role of E3 in sumoylation.
  PLoS Comput Biol, 6, 0.  
18693244 K.Palle, L.Pattarello, M.van der Merwe, C.Losasso, P.Benedetti, and M.A.Bjornsti (2008).
Disulfide cross-links reveal conserved features of DNA topoisomerase I architecture and a role for the N terminus in clamp closure.
  J Biol Chem, 283, 27767-27775.  
  18949077 L.Eun Jeoung, H.Sung Hee, C.Jaesun, S.Sung Hwa, Y.Kwang Hum, K.Min Kyoung, P.Tae Yoon, and K.Sang Sun (2008).
Regulation of glycogen synthase kinase 3beta functions by modification of the small ubiquitin-like modifier.
  Open Biochem J, 2, 67-76.  
18703419 M.Ihara, P.Stein, and R.M.Schultz (2008).
UBE2I (UBC9), a SUMO-conjugating enzyme, localizes to nuclear speckles and stimulates transcription in mouse oocytes.
  Biol Reprod, 79, 906-913.  
17475278 D.M.Duda, R.C.van Waardenburg, L.A.Borg, S.McGarity, A.Nourse, M.B.Waddell, M.A.Bjornsti, and B.A.Schulman (2007).
Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a non-covalent ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway.
  J Mol Biol, 369, 619-630.
PDB code: 2eke
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